This paper reports on the mechanistic basis of cellular death in the testis of Clarias gariepinus using the TUNEL and caspase-3 immunohistochemistry. It was also aimed to determine the testicular zone most suitable for the quantification of testicular apoptosis. The results showed that based on its immuno-expression patterns, activated caspase-3 has a clear and defined role in the progression of germ cell apoptosis in spermatogenically active catfish testis. Caspase-3 activation, and not TUNEL-detected DNA fragmentation, is associated with condensation of chromatin into a single mass. Testes of spermatogenically active catfish consist of spermatogenic, mature and spent tubules. Spermatogenic tubules were concluded to be the most suitable zone for the quantification of testicular cell death ratios as apoptotic events occurred predominantly in the secondary spermatocytes. The findings of this study will form the basis to link apoptotic events in the testes of C. gariepinus with the effects of EDC exposure in future studies.